Indirect measurement of mutation rate was pioneered by Luria and Delbruck in their classic Fluctuation Test (Luria and Delbruck 1943). The concept of measuring somatic mutation by quantifying the number of cells that show phenotypic changes was extended to human cells, using genes such as HLA, HPRT or TK. Albertini et al. 1990, the disclosure of which is incorporated by reference in its entirety herein. A lacZ reporter assay was developed for model organisms such as mouse or fly of which transgenic progenies can be made (Garcia et al. 2007, the disclosure of which is incorporated by reference in its entirety herein). Such indirect assays typically assume a constant level of penetrance for mutations, which can be problematic. In addition, the indirect measurement of mutation rate in a kilobase-size locus is extrapolated to the entire genome, based on an oversimplified assumption of constant mutation rate throughout the genome. These limitations call for direct measurements of mutation rate in human cells genome-wide. The germline mutation rate in human was directly measured very recently (Roach et al. 2010, the disclosure of which is incorporated by reference in its entirety herein), yet direct measuring of somatic mutation rate genome-wide remains to be demonstrated almost 80 years after the Luria-Delbruck experiment.
Rapid advances in DNA sequencing technology have made it possible for routine de novo sequencing of many organisms, and re-sequencing of human individuals or human cancers. Single cell sequencing experiments have been described in Marcy et al. 2007 and Fan et al. Nature Biotechnology, 2011, 29:51-57, the disclosure of which is incorporated by reference in its entirety herein.